Error loading `extension ROTATIONS` from Pulseq 1.5.1

[spinicist]

What happened?

Hello,

I'm trying to load a Pulseq file generated with https://github.com/fmrifrey/lps into Koma.jl. This produces the error:

julia> [ Info: Loading sequence lps.seq ...
use occursin(needle, haystack) for string containment
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] in(::SubString{String}, ::String)
    @ Base ./strings/search.jl:809
  [3] read_extensions(io::IOStream, ext_string::SubString{String}, ext_type::Nothing, ext_id::Int64, extensionTypeLibrary::Dict{Any, Any}, extensionSpecLibrary::Dict{Any, Any}, required_extensions::String)
    @ KomaMRIFiles ~/.julia/packages/KomaMRIFiles/mCkCM/src/Sequence/Pulseq.jl:160
  [4] (::KomaMRIFiles.var"#read_seq##0#read_seq##1"{Dict{Any, Any}, Dict{Any, Any}})(io::IOStream)
    @ KomaMRIFiles ~/.julia/packages/KomaMRIFiles/mCkCM/src/Sequence/Pulseq.jl:449
  [5] open(f::KomaMRIFiles.var"#read_seq##0#read_seq##1"{Dict{Any, Any}, Dict{Any, Any}}, args::String; kwargs::@Kwargs{})
    @ Base ./io.jl:410
  [6] read_seq(filename::String)
    @ KomaMRIFiles ~/.julia/packages/KomaMRIFiles/mCkCM/src/Sequence/Pulseq.jl:378
  [7] callback_filepicker(filename::String, w::Blink.AtomShell.Window, seq::Sequence)
    @ KomaMRI ~/.julia/packages/KomaMRI/i4er5/src/ui/ExportUIFunctions.jl:172
  [8] (::KomaMRI.var"#127#128"{Blink.AtomShell.Window})(filename::String)
    @ KomaMRI ~/.julia/packages/KomaMRI/i4er5/src/KomaUI.jl:283
  [9] (::Observables.MapCallback)(value::Any)
    @ Observables ~/.julia/packages/Observables/YdEbO/src/Observables.jl:436
 [10] set_nosync(ob::Observables.Observable{Any}, val::String)
    @ WebIO ~/.julia/packages/WebIO/8Xm9p/src/scope.jl:346
 [11] dispatch(ctx::WebIO.Scope, key::String, data::String)
    @ WebIO ~/.julia/packages/WebIO/8Xm9p/src/scope.jl:358
 [12] dispatch_command(conn::Blink.AtomShell.WebIOBlinkComm, data::Dict{String, Any})
    @ WebIO ~/.julia/packages/WebIO/8Xm9p/src/messaging.jl:104
 [13] dispatch(conn::Blink.AtomShell.WebIOBlinkComm, data::Dict{String, Any})
    @ WebIO ~/.julia/packages/WebIO/8Xm9p/src/messaging.jl:81
 [14] (::Blink.AtomShell.var"#initwebio!##0#initwebio!##1"{Blink.AtomShell.WebIOBlinkComm})(msg::Dict{String, Any})
    @ Blink.AtomShell ~/.julia/packages/Blink/tnO3a/src/AtomShell/webio.jl:29
 [15] handle_message(o::Blink.Page, m::Dict{String, Any})
    @ Blink ~/.julia/packages/Blink/tnO3a/src/rpc/callbacks.jl:7
 [16] macro expansion
    @ ~/.julia/packages/Lazy/9Xnd3/src/macros.jl:268 [inlined]
 [17] ws_handler(ws::HTTP.WebSockets.WebSocket)
    @ Blink ~/.julia/packages/Blink/tnO3a/src/content/server.jl:50
 [18] (::Mux.var"#ws_handler##0#ws_handler##1"{Mux.App})(sock::HTTP.WebSockets.WebSocket)
    @ Mux ~/.julia/packages/Mux/u4vsZ/src/server.jl:48
 [19] upgrade(f::Mux.var"#ws_handler##0#ws_handler##1"{Mux.App}, http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.Connections.Connection{Sockets.TCPSocket}}; suppress_close_error::Bool, maxframesize::Int64, maxfragmentation::Int64, nagle::Bool, quickack::Bool, kw::@Kwargs{})
    @ HTTP.WebSockets ~/.julia/packages/HTTP/ShTJs/src/WebSockets.jl:427
 [20] (::Mux.var"#10#11"{Mux.App, Mux.App})(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.Connections.Connection{Sockets.TCPSocket}})
    @ Mux ~/.julia/packages/Mux/u4vsZ/src/server.jl:80
 [21] handle_connection(f::Function, c::HTTP.Connections.Connection{Sockets.TCPSocket}, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing, verbose::Bool)
    @ HTTP.Servers ~/.julia/packages/HTTP/ShTJs/src/Servers.jl:469
 [22] (::HTTP.Servers.var"#listenloop##0#listenloop##1"{Mux.var"#10#11"{Mux.App, Mux.App}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.Connections.Connection}, Int64, Nothing, ReentrantLock, Bool, Base.Semaphore, HTTP.Connections.Connection{Sockets.TCPSocket}})()
    @ HTTP.Servers ~/.julia/packages/HTTP/ShTJs/src/Servers.jl:400

I have attached the .seq file. Any help much appreciated.

lps.tar.gz

Environment

OS arm64-apple-darwin24.0.0
Julia 1.12.5
KomaMRIPlots 0.9.6
KomaMRIFiles 0.9.9
KomaMRI 0.9.2
KomaMRICore 0.9.6
KomaMRIBase 0.9.8

[cncastillo]

H! Thanks for using Koma and reporting this issue!

It seems to be failing reading some extensions

# Extension specification for setting labels:
# id set labelstring
extension LABELSET 2
1 2 TRID
2 3 TRID
3 1 TRID

# Extension specification for rotation events:
# id RotQuat0 RotQuatX RotQuatY RotQuatZ
extension ROTATIONS 1
1  0.474662 -0.736136 0.405504 -0.26147
2  0.301665 0.665882 -0.621542 -0.281578
3  0.543231 0.0806243 -0.122688 -0.826648
...

We don't have all extensions implemented, but it shouldn't fail to load, it should trigger a message Pulseq v1.5.1 is supported, but Soft Delay, Rotation, and RF Shimming extensions are not yet included (see https://github.com/JuliaHealth/KomaMRI.jl/issues/714).

@spinicist Could you remove the ROTATIONS events just to test if that is what it's failing? I don't think is the LABELSET.

We spent some time designing the extension system so it is extensible, so adding a new one should be simple, this is how TRIGGERS are defined:

KomaMRI.jl/KomaMRIBase/src/datatypes/sequence/extensions/Trigger.jl

Lines 1 to 10 in 21a7c25

	mutable struct Trigger <: Extension
	type::Int # Type of trigger (system dependent). 0: undefined / unused
	channel::Int # channel of trigger (system dependent). 0: undefined / unused
	d1::Float64 # Delay prior to the trigger event [s]
	d2::Float64 # Duration of trigger event [s]
	end
	get_scale(::Type{Trigger}) = [1 1 1e-6 1e-6]
	get_scanf_format(::Type{Trigger}) = "%i %i %f %f"
	get_EXT_type_from_symbol(::Val{:TRIGGERS}) = Trigger

In theory, implementing rotations (just for the reader) should look something like this

mutable struct Rotation <: KomaMRIBase.Extension 
    RotQuat0::Float64
    RotQuatX::Float64
    RotQuatY::Float64
    RotQuatZ::Float64
end

KomaMRIBase.get_scale(::Type{Rotation}) = [1.0 1.0 1.0 1.0]
KomaMRIBase.get_scanf_format(::Type{Rotation}) = "%f %f %f %f"
KomaMRIBase.get_EXT_type_from_symbol(::Val{:ROTATIONS}) = Rotation

@pvillacorta could you check this one out? I don't think this should fail. Unrelated: Also why are these structs mutable?

[spinicist]

Thanks for the quick response. The rotations are a fundamental part of the sequence. I couldn't see a straightforward way to remove them as they are associated with each block: https://github.com/fmrifrey/lps/blob/master/lps_write_seq.m#L157. I think I'd have to edit Pulseq itself?

(I'm not the author of that repo)

[cncastillo]

Ok, I just confirmed that the problem was the ROTATIONS extension, and after adding it like this:

mutable struct Rotation <: KomaMRIBase.Extension 
    RotQuat0::Float64
    RotQuatX::Float64
    RotQuatY::Float64
    RotQuatZ::Float64
end

KomaMRIBase.get_scale(::Type{Rotation}) = [1.0 1.0 1.0 1.0]
KomaMRIBase.get_scanf_format(::Type{Rotation}) = "%f %f %f %f"
KomaMRIBase.get_EXT_type_from_symbol(::Val{:ROTATIONS}) = Rotation

I can read the file correctly. So you can try that right now to read the rotations without crashing, but the gradients in the sequence will not be rotated yet.

As it is not too difficult, between today and tomorrow I will try to implement rotations correctly so they are applied to the sequence.

@spinicist do you mind if we use this file as part of the tests?

[pvillacorta]

See #729